Aside

Océane Cassan

Contact

Skills

Biology : gene regulation, plant systems biology, Next Generation Sequencing data analysis

Computer science : R (ggplot, tidyverse, package developement, Rmarkdown, Shiny) Python, LaTeX-beamer, Bash, calculation server administration and usage, web application deployment

Disclaimer

Main

Océane Cassan

Currently searching for a postdoctoral position

Education

University Claude Bernard (UCBL)

MSc in Computer Science - Artificial Intelligence

Lyon, France

2019 - 2018

National Institute of Applied Sciences (INSA)

Engineering degree in Bioinformatics and Modelling

Lyon, France

2019 - 2014

Research Experience

PhD - Institute for Plant Sciences in Montpellier

Predictive biology to learn the regulatory pathways in plants under climate change, SIRENE team

Montpellier, France

2022 - 2019

  • Statistical inference of the gene regulatory networks in Arabidopsis thaliana under elevated CO\(_2\) and nutritional limitations. Network reconstruction via ensembles of regression trees or penalized linear regression based using transcriptomic data and regulatory sequences information. Computational and experimental validation of network-derived hypotheses and candidate genes.
  • Genome Wide Association studies to identify genetic determinants of mineral status repsonse under elevated CO\(_2\)
  • Developement of an interactive suite for transcriptomic analyses and the inference of regulatory networks

6 months research internship - LIRMM, MAB team

Supervised learning to predict chromosomic interactions in the human genome, based on CAGE data and 3C techniques

Montpellier, France

2019

1 month research internship - LIRMM, MAB team

Sparse logistic regression to model transcription factor combinatorics for gene regulation in human

Montpellier, France

2017

Professional Experience

Internship in quantitative biology - Nanolive SA

Development of software tools for the 3D detection and tracking of biological objects in label free images

Lausanne, Switzerland

2018

Teaching Experience

Instructor of R for L3 plant biology students

Teaching material

University of Montpellier, France

2022 - 2021

  • Good practices and scientific integrity around data analysis
  • Data manipulation and visualisation in R

Instructor of Rmarkdown for M1 data science students

Teaching material

University Paul Valery of Montpellier, France

2022 - 2020

Regulatory network inference for M1 plant biology students

Statistics and regression techniques for network inference.

University of Montpellier, France

2022

Student supervision

N/A

N/A

2021 - 2022

  • M2 intern in biostatistics appied to gene regulation and transcriptomics
  • M1 data science stduents for an annual project on Genome-Wide-Association studies

Selected Publications

Inferring and Analyzing Gene Regulatory Networks from Multi-Factorial Expression Data: A Complete and Interactive Suite

Cassan, Océane, Sophie Lèbre, and Antoine Martin. 2021 BMC Genomics 22 (1). See article

N/A

2021

Probing Transcription Factor Combinatorics in Different Promoter Classes and in Enhancers

Vandel, Jimmy, Océane Cassan, Sophie Lèbre, Charles-Henri Lecellier, and Laurent Bréhélin. 2019 BMC Genomics 20 (1): 1–19. See article

N/A

2019

Conferences and workshops

Molecular responses of plants facing climate change

Organizer and presenter

Montpellier, France

2022

  • Poster presenting genetic determinants to mineral status response under elevated CO2 in Arabidopsis populations

JOBIM

Presenter

Virtual

2021

  • Poster presenting the Dashboard for the Inference and Analysis of Networks from Expression data

International Plant Systems Biology

Presenter

Virtual

2021

  • Poster presenting Gene Regulatory Network inference of Arabidopsis under eCO2 and nutritional limitations

Netbio

Speaker

Virtual

2020

  • Talk presenting the Dashboard for the Inference and Analysis of Networks from Expression data

Academic referees

Antoine Martin, senior researcher in plant biology, head of SIRENE team, IPSiM, CNRS :

Sophie Lèbre, lecturer and researcher in statistics, IMAG, University of Montpellier, University Paul Valéry :

Laurent Bréhélin, senior researcher in computational biology, head of MAB team, LIRMM :